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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_012592
Reference: OH-1004 Chr: Chr03 Coordinates: 15238359-15247981 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

4536 bp · LXL04_012592|LXL04_012592|OH1004|cDNA

ATGGTGGATAAGGGAAAAGGGATCGCTGATGATTATTCATCGGGGAAACGGAAACGCCACGGAGAAGATAAATCTGCTCATCCAAAGAGAAAAAACCTCAATGTCCTTCAGTTCTTCGAGGATTCCGCCTTCGAAGTAGACGAGAGCGATTCTAGTGACGATGACGTTTTTATAAATGATGGTATAGACATTAGTAACTCTTCCGATCATCGTCATTGTTTGCATTTTGACACTATATTTTTTGTCATTTTAGGATTTCT...

CDS

Download CDS FASTA

4536 bp · LXL04_012592|LXL04_012592|OH1004|CDS

ATGGTGGATAAGGGAAAAGGGATCGCTGATGATTATTCATCGGGGAAACGGAAACGCCACGGAGAAGATAAATCTGCTCATCCAAAGAGAAAAAACCTCAATGTCCTTCAGTTCTTCGAGGATTCCGCCTTCGAAGTAGACGAGAGCGATTCTAGTGACGATGACGTTTTTATAAATGATGGTATAGACATTAGTAACTCTTCCGATCATCGTCATTGTTTGCATTTTGACACTATATTTTTTGTCATTTTAGGATTTCT...

Protein

Download Protein FASTA

1511 aa · LXL04_012592|LXL04_012592|OH1004|PROTEIN

MVDKGKGIADDYSSGKRKRHGEDKSAHPKRKNLNVLQFFEDSAFEVDESDSSDDDVFINDGIDISNSSDHRHCLHFDTIFFVILGFLGVYSSHVKFTYCSFAAVVFLEDDFGPDIDVKAEPKTPNMPFFPKEEDMDVEELDRILEERYKPGSNFVKYAEDRATEAPRSDDRDTLMSHVVEPKIWKVKCMVGRERHSAFCLMQKYVDLQALGTKLEIVSAFAVEHVKGFIYIEAEKQSACSGLCNIYPSRVSPIPVSDVPH...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

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ID Mapping

Input IDLXL04_012592
TK1151 IDTkA02G551200
OH-1004 IDLXL04_012592
Relationship / confidenceRbh Sequence Supported / Probable
Protein identity (%)93.100
Protein coverage (%)TK1151 99.859 / OH-1004 93.183
Coverage and evidence

Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.

Source versionOH-1004 / GCA_047496595.1_OSU_TarKok_2.0
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDLXL04_012592
LocationChr03:15238359-15247981 (+)
DescriptionSimilar to RDM3: Protein RNA-directed DNA methylation 3
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g04290 Effector of RNA-directed DNA methylation (RdDM) triggered by small interfering RNAs (siRNAs, 24-nt RNAs).
An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein.2009 · DOI: 10.1016/j.cell.2009.04.028
Identification of genes required for de novo DNA methylation in Arabidopsis.2011 · DOI: 10.4161/epi.6.3.14242
Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing.2011 · DOI: 10.1371/journal.pgen.1002120
At4g08350 May regulate transcription elongation by RNA polymerase II. No verified direct reference in this release
At2g34210 May regulate transcription elongation by RNA polymerase II. No verified direct reference in this release
At4g36020 Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex.
Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli.2007 · DOI: 10.1093/nar/gkl1076
Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions.2009 · DOI: 10.1093/pcp/pcp037

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_012592 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006357 regulation of transcription by RNA polymerase II Biological Process
GO:0006368 transcription elongation by RNA polymerase II Biological Process
GO:0030422 siRNA processing Biological Process
GO:0031507 heterochromatin formation Biological Process
GO:0032784 regulation of DNA-templated transcription elongation Biological Process
GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process
GO:0005634 nucleus Cellular Component
GO:0005654 nucleoplasm Cellular Component
GO:0032044 DSIF complex Cellular Component
GO:0003677 DNA binding Molecular Function
GO:0003682 chromatin binding Molecular Function
GO:0003723 RNA binding Molecular Function
KEGG gene cross-reference
ath:AT5G04290
These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.
Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene
Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.877
Rank 1 · LXL04_012592 · OH-1004
Cytoplasm0.191
Rank 2 · LXL04_012592 · OH-1004
Cell membrane0.042
Rank 3 · LXL04_012592 · OH-1004
Endoplasmic reticulum0.030
Rank 4 · LXL04_012592 · OH-1004
Mitochondrion0.023
Rank 5 · LXL04_012592 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF03439.19Spt5-NGN182-262 aa
PF23042.3KOW1_SPT5271-396 aa
PF00467.36KOW274-304 aa
PF23037.2KOWx_SPT5440-491 aa
PF23291.2KOW4_SPT5500-554 aa
PF00098.29zf-CCHC1005-1021 aa
PF00098.29zf-CCHC1031-1047 aa
PF00098.29zf-CCHC1057-1073 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_012592PF03439.19Spt5-NGN1822627.8e-1761.7
LXL04_012592PF23042.3KOW1_SPT52713966e-2485.8
LXL04_012592PF00467.36KOW2743042e-0834.4
LXL04_012592PF23037.2KOWx_SPT54404911.8e-0628.2
LXL04_012592PF23291.2KOW4_SPT55005542.8e-2072.7
LXL04_012592PF00098.29zf-CCHC100510213.6e-73239.3
LXL04_012592PF00098.29zf-CCHC103110473.6e-73239.3
LXL04_012592PF00098.29zf-CCHC105710733.6e-73239.3
LXL04_012592PF00098.29zf-CCHC108411003.6e-73239.3
LXL04_012592PF00098.29zf-CCHC110711233.6e-73239.3
LXL04_012592PF00098.29zf-CCHC113511513.6e-73239.3
LXL04_012592PF00098.29zf-CCHC116211783.6e-73239.3
LXL04_012592PF00098.29zf-CCHC118712043.6e-73239.3
LXL04_012592PF00098.29zf-CCHC121512313.6e-73239.3
LXL04_012592PF00098.29zf-CCHC124212583.6e-73239.3

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

ProteinOrganismDescriptionIdentityDatabaseConfidence
F4JW79Arabidopsis thalianaProtein RNA-directed DNA methylation 340.000%Swiss-Protmoderate database homology
Q9STN3Arabidopsis thalianaPutative transcription elongation factor SPT5 homolog 141.806%Swiss-Protweak database homology
O80770Arabidopsis thalianaPutative transcription elongation factor SPT5 homolog 240.803%Swiss-Protweak database homology
O65639Arabidopsis thalianaCold shock protein 141.176%Swiss-Protweak database homology

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